feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
Documentation: - Add docs/06_PHYSICS/ with Zernike fundamentals and OPD method docs - Add docs/guides/CMA-ES_EXPLAINED.md optimization guide - Update CLAUDE.md and ATOMIZER_CONTEXT.md with current architecture - Update OP_01_CREATE_STUDY protocol Planning: - Add DYNAMIC_RESPONSE plans for random vibration/PSD support - Add OPTIMIZATION_ENGINE_MIGRATION_PLAN for code reorganization Insights System: - Update design_space, modal_analysis, stress_field, thermal_field insights - Improve error handling and data validation NX Journals: - Add analyze_wfe_zernike.py for Zernike WFE analysis - Add capture_study_images.py for automated screenshots - Add extract_expressions.py and introspect_part.py utilities - Add user_generated_journals/journal_top_view_image_taking.py Tests & Tools: - Add comprehensive Zernike OPD test suite - Add audit_v10 tests for WFE validation - Add tools for Pareto graphs and mirror data extraction - Add migrate_studies_to_topics.py utility Knowledge Base: - Initialize LAC (Learning Atomizer Core) with failure/success patterns Dashboard: - Update Setup.tsx and launch_dashboard.py - Add restart-dev.bat helper script 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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tools/extract_mirror_optical_specs.py
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294
tools/extract_mirror_optical_specs.py
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#!/usr/bin/env python
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"""
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Extract Mirror Optical Specifications from FEA Mesh Geometry
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This tool analyzes mirror mesh geometry to estimate optical specifications
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including focal length, aperture diameter, f-number, and radius of curvature.
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Usage:
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# From study directory containing OP2 files
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python -m optimization_engine.tools.extract_mirror_optical_specs .
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# From specific OP2 file
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python -m optimization_engine.tools.extract_mirror_optical_specs path/to/results.op2
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# Save to study README
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python -m optimization_engine.tools.extract_mirror_optical_specs . --update-readme
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Output:
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- Console: Optical specifications summary
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- Optional: Updates parent README.md with validated specs
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Author: Atomizer Framework
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"""
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from pathlib import Path
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import argparse
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import sys
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# Add project root to path (tools/ is at project root, so parent is Atomizer/)
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sys.path.insert(0, str(Path(__file__).parent.parent))
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import numpy as np
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def find_op2_file(path: Path) -> Path:
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"""Find an OP2 file from path (file or directory)."""
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path = Path(path)
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if path.is_file() and path.suffix.lower() == '.op2':
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return path
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if path.is_dir():
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# Look in common locations
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search_patterns = [
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'**/2_iterations/**/*.op2',
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'**/*.op2',
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'2_iterations/**/*.op2',
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'1_setup/model/*.op2',
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]
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for pattern in search_patterns:
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op2_files = list(path.glob(pattern))
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if op2_files:
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# Return most recent
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return max(op2_files, key=lambda p: p.stat().st_mtime)
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raise FileNotFoundError(f"No OP2 file found in {path}")
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def extract_optical_specs(op2_path: Path, verbose: bool = True) -> dict:
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"""
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Extract optical specifications from mirror mesh geometry.
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Args:
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op2_path: Path to OP2 file
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verbose: Print detailed output
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Returns:
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dict with optical specifications
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"""
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from optimization_engine.extractors.extract_zernike_opd import (
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ZernikeOPDExtractor,
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estimate_focal_length_from_geometry
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)
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if verbose:
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print(f"Analyzing: {op2_path}")
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print("=" * 60)
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extractor = ZernikeOPDExtractor(op2_path)
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# Get geometry
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geo = extractor.node_geometry
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all_pos = np.array(list(geo.values()))
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x, y, z = all_pos[:, 0], all_pos[:, 1], all_pos[:, 2]
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# Compute radius/diameter
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r = np.sqrt(x**2 + y**2)
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# Estimate focal length
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focal = estimate_focal_length_from_geometry(x, y, z, concave=True)
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# Derived quantities
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diameter = 2 * r.max()
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f_number = focal / diameter
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RoC = 2 * focal # Radius of curvature
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sag = r.max()**2 / (4 * focal) # Surface sag at edge
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central_obs = r.min() if r.min() > 1.0 else 0.0 # Central obscuration
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# Parabola fit quality check
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r_sq = x**2 + y**2
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A = np.column_stack([r_sq, np.ones_like(r_sq)])
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coeffs, _, _, _ = np.linalg.lstsq(A, z, rcond=None)
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a, b = coeffs
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z_fit = a * r_sq + b
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rms_error = np.sqrt(np.mean((z - z_fit)**2))
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# Determine fit quality
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if rms_error < 0.1:
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fit_quality = "Excellent"
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fit_note = "Focal length estimate is reliable"
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elif rms_error < 1.0:
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fit_quality = "Good"
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fit_note = "Focal length estimate is reasonably accurate"
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else:
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fit_quality = "Poor"
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fit_note = "Consider using explicit focal length from optical design"
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specs = {
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'aperture_diameter_mm': diameter,
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'aperture_radius_mm': r.max(),
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'focal_length_mm': focal,
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'f_number': f_number,
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'radius_of_curvature_mm': RoC,
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'surface_sag_mm': sag,
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'central_obscuration_mm': central_obs,
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'node_count': len(geo),
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'x_range_mm': (x.min(), x.max()),
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'y_range_mm': (y.min(), y.max()),
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'z_range_mm': (z.min(), z.max()),
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'parabola_fit_rms_mm': rms_error,
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'fit_quality': fit_quality,
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'fit_note': fit_note,
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'source_file': str(op2_path),
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}
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if verbose:
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print()
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print("MIRROR OPTICAL SPECIFICATIONS (from mesh geometry)")
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print("=" * 60)
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print()
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print(f"Aperture Diameter: {diameter:.1f} mm ({diameter/1000:.3f} m)")
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print(f"Aperture Radius: {r.max():.1f} mm")
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if central_obs > 0:
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print(f"Central Obscuration: {central_obs:.1f} mm")
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print()
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print(f"Estimated Focal Length: {focal:.1f} mm ({focal/1000:.3f} m)")
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print(f"Radius of Curvature: {RoC:.1f} mm ({RoC/1000:.3f} m)")
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print(f"f-number (f/D): f/{f_number:.2f}")
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print()
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print(f"Surface Sag at Edge: {sag:.2f} mm")
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print()
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print("--- Mesh Statistics ---")
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print(f"Node count: {len(geo)}")
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print(f"X range: {x.min():.1f} to {x.max():.1f} mm")
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print(f"Y range: {y.min():.1f} to {y.max():.1f} mm")
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print(f"Z range: {z.min():.2f} to {z.max():.2f} mm")
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print()
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print("--- Parabola Fit Quality ---")
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print(f"RMS fit residual: {rms_error:.4f} mm ({rms_error*1000:.2f} µm)")
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print(f"Quality: {fit_quality} - {fit_note}")
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print()
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print("=" * 60)
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return specs
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def generate_readme_section(specs: dict) -> str:
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"""Generate markdown section for README."""
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return f"""## 2. Optical Prescription
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> **Source**: Estimated from mesh geometry. Validate against optical design.
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| Parameter | Value | Units | Status |
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|-----------|-------|-------|--------|
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| Aperture Diameter | {specs['aperture_diameter_mm']:.1f} | mm | Estimated |
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| Focal Length | {specs['focal_length_mm']:.1f} | mm | Estimated |
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| f-number | f/{specs['f_number']:.2f} | - | Computed |
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| Radius of Curvature | {specs['radius_of_curvature_mm']:.1f} | mm | Computed (2×f) |
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| Central Obscuration | {specs['central_obscuration_mm']:.1f} | mm | From mesh |
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| Surface Type | Parabola | - | Assumed |
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**Fit Quality**: {specs['fit_quality']} ({specs['fit_note']})
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### 2.1 Usage in OPD Extractor
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For rigorous WFE analysis, use explicit focal length:
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```python
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from optimization_engine.extractors import ZernikeOPDExtractor
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extractor = ZernikeOPDExtractor(
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op2_file,
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focal_length={specs['focal_length_mm']:.1f}, # mm - validate against design
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concave=True
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)
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```
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"""
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def update_readme(study_dir: Path, specs: dict):
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"""Update parent README with optical specs."""
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readme_path = study_dir / 'README.md'
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if not readme_path.exists():
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print(f"README.md not found at {readme_path}")
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return False
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content = readme_path.read_text(encoding='utf-8')
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# Find and replace optical prescription section
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new_section = generate_readme_section(specs)
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# Look for existing section
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import re
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pattern = r'## 2\. Optical Prescription.*?(?=## 3\.|$)'
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if re.search(pattern, content, re.DOTALL):
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content = re.sub(pattern, new_section + '\n---\n\n', content, flags=re.DOTALL)
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print(f"Updated optical prescription in {readme_path}")
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else:
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print(f"Could not find '## 2. Optical Prescription' section in {readme_path}")
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print("Please add manually or check section numbering.")
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return False
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readme_path.write_text(content, encoding='utf-8')
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return True
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def main():
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parser = argparse.ArgumentParser(
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description='Extract mirror optical specifications from FEA mesh',
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formatter_class=argparse.RawDescriptionHelpFormatter,
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epilog="""
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Examples:
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# Analyze current study directory
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python -m optimization_engine.tools.extract_mirror_optical_specs .
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# Analyze specific OP2 file
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python -m optimization_engine.tools.extract_mirror_optical_specs results.op2
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# Update parent README with specs
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python -m optimization_engine.tools.extract_mirror_optical_specs . --update-readme
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"""
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)
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parser.add_argument('path', type=str,
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help='Path to OP2 file or study directory')
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parser.add_argument('--update-readme', action='store_true',
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help='Update parent README.md with optical specs')
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parser.add_argument('--quiet', '-q', action='store_true',
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help='Suppress detailed output')
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parser.add_argument('--json', action='store_true',
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help='Output specs as JSON')
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args = parser.parse_args()
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try:
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path = Path(args.path).resolve()
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op2_path = find_op2_file(path)
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specs = extract_optical_specs(op2_path, verbose=not args.quiet and not args.json)
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if args.json:
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import json
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print(json.dumps(specs, indent=2, default=str))
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if args.update_readme:
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# Find study root (parent of geometry type folder)
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study_dir = path if path.is_dir() else path.parent
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# Go up to geometry type level
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while study_dir.name not in ['studies', ''] and not (study_dir / 'README.md').exists():
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if (study_dir.parent / 'README.md').exists():
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study_dir = study_dir.parent
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break
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study_dir = study_dir.parent
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if (study_dir / 'README.md').exists():
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update_readme(study_dir, specs)
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else:
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print(f"Could not find parent README.md to update")
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except FileNotFoundError as e:
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print(f"Error: {e}")
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sys.exit(1)
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except Exception as e:
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print(f"Error: {e}")
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import traceback
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traceback.print_exc()
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sys.exit(1)
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if __name__ == '__main__':
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main()
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